feat: initial state

#!/bin/bash

TARGET_EXEC ?= mcPolymer

KMCTEST_EXEC ?= kmcTest

CEMPOLY_EXEC ?= cempoly

DBUSSERVER_EXEC ?= mcPolymerDBusServer

ANALYSIS_EXEC ?= analysis

MCPSIM_MAIN ?= mcPolymerCmdl.cpp

MCPSIM_SO ?= ./build/lib/libmcPolymer.so

CEMPOLY_SO ?= ./build/lib/cempoly.so

BUILD_DIR ?= ./build

SRC_DIRS ?= ./src

SRC_COMMON ?= ./src/common

SRC_MCPSIM ?= $(SRC_COMMON) ./src/mcPolymerSim

SRC_KMCLIB ?= $(SRC_COMMON) ./src/kmclib

SRC_CEMPOLY ?= $(SRC_COMMON) ./src/cempoly

SRC_ANALYSIS ?= $(SRC_COMMON) ./src/analysis

SRC_DBUSSERVER ?= $(SRC_COMMON) ./src/mcpolymer-d-bus

SRC_INC ?= ./src

COVERAGE ?=

COVERAGE_DIR ?= ./coverage

LOG_DIR ?= ./log

CXX ?= mpicxx

MPICXX ?= mpicxx

SRCS_MCPSIM := $(shell find $(SRC_MCPSIM) -name *.cpp -or -name *.c)

SRCS_MCPSIM_SO := $(filter-out $(SRC_MCPSIM)/$(MCPSIM_MAIN), $(SRCS_MCPSIM))

OBJS_MCPSIM := $(SRCS_MCPSIM:%=$(BUILD_DIR)/%.o)

OBJS_MCPSIM_SO := $(SRCS_MCPSIM_SO:%=$(BUILD_DIR)/%.o)

DEPS_MCPSIM := $(OBJS_MCPSIM:.o=.d)

SRCS_KMCLIB := $(shell find $(SRC_KMCLIB) -name *.cpp -or -name *.c)

OBJS_KMCLIB := $(SRCS_KMCLIB:%=$(BUILD_DIR)/%.o)

DEPS_KMCLIB := $(OBJS_KMCLIB:.o=.d)

SRCS_CEMPOLY := $(shell find $(SRC_CEMPOLY) -name *.cpp -or -name *.c)

OBJS_CEMPOLY := $(SRCS_CEMPOLY:%=$(BUILD_DIR)/%.o)

DEPS_CEMPOLY := $(OBJS_CEMPOLY:.o=.d)

SRCS_DBUSSERVER := $(shell find $(SRC_DBUSSERVER) -name *.cpp -or -name *.c)

OBJS_DBUSSERVER := $(SRCS_DBUSSERVER:%=$(BUILD_DIR)/%.o)

DEPS_DBUSSERVER := $(OBJS_DBUSSERVER:.o=.d)

SRCS_ANALYSIS := $(shell find $(SRC_ANALYSIS) -name *.cpp -or -name *.c)

OBJS_ANALYSIS := $(SRCS_ANALYSIS:%=$(BUILD_DIR)/%.o)

DEPS_ANALYSIS := $(OBJS_ANALYSIS:.o=.d)

GTEST_EXEC := gtest

GTEST_SRC := $(SRC_DIRS)/gtest

GTEST_SRCS := $(shell find $(GTEST_SRC) -name *.cpp -or -name *.c)

GTEST_LIB := gtest

GTEST_COVFLAGS := --coverage -fprofile-arcs -ftest-coverage

GTEST_LDFLAGS := -L$(dir $(MCPSIM_SO)) -l$(GTEST_LIB) -lpthread -lmcPolymer -lmpi

INC_DIRS := $(shell find $(SRC_DIRS) -type d) /usr/lib/x86_64-linux-gnu/openmpi/include /usr/include/dbus-1.0 /usr/lib/x86_64-linux-gnu/dbus-1.0/include

INC_FLAGS := $(addprefix -I,$(INC_DIRS))

CPPFLAGS ?= $(INC_FLAGS) -O3 -fPIC -std=c++17 -Wall -Werror 

LDFLAGS ?= -lm -pthread -lstdc++

$(TARGET_EXEC): $(OBJS_MCPSIM)

	$(CC) $(OBJS_MCPSIM) -o $@ $(LDFLAGS)

$(KMCTEST_EXEC): $(OBJS_KMCLIB)

	$(CC) $(OBJS_KMCLIB) -o $@ $(LDFLAGS)

$(MCPSIM_SO): $(OBJS_MCPSIM_SO)

	$(MKDIR_P) $(dir $@)

	$(CC) -shared -o $@ $(OBJS_MCPSIM_SO) $(COVERAGE)

$(CEMPOLY_SO): $(OBJS_CEMPOLY)

	$(MKDIR_P) $(dir $@)

	$(CC) -shared -o $@ $(OBJS_CEMPOLY) $(COVERAGE)

$(GTEST_EXEC): $(GTEST_SRCS) $(MCPSIM_SO)

	$(CXX) $(CPPFLAGS) $(CXXFLAGS) -o $@ $(GTEST_COVFLAGS) $(GTEST_SRCS) $(GTEST_LDFLAGS)

	# cleanup leftovers of failing run

	rm *.gc*

	$(MKDIR_P) build/gtest

	LD_LIBRARY_PATH=$(LD_LIBRARY_PATH):$(dir $(MCPSIM_SO)) ./$(GTEST_EXEC)

	rm *.gc*

$(CEMPOLY_EXEC): $(OBJS_CEMPOLY) $(MCPSIM_SO)

	$(MPICXX) $(OBJS_CEMPOLY) -o $@ $(GTEST_LDFLAGS)

$(DBUSSERVER_EXEC): $(OBJS_DBUSSERVER) $(MCPSIM_SO)

	$(MPICXX) $(OBJS_DBUSSERVER) -o $@ $(GTEST_LDFLAGS)

$(ANALYSIS_EXEC): $(OBJS_ANALYSIS) $(MCPSIM_SO)

	$(MPICXX) $(OBJS_ANALYSIS) -o $@ $(GTEST_LDFLAGS)

all: $(GTEST_EXEC) $(TARGET_EXEC) $(KMCTEST_EXEC) $(CEMPOLY_EXEC) $(ANALYSIS_EXEC)

debug: CPPFLAGS := $(filter-out -O%, $(CPPFLAGS)) -O0 -ggdb

debug: $(TARGET_EXEC)

coverage: COVERAGE= --coverage

coverage: $(GTEST_EXEC)

	$(MKDIR_P) $(COVERAGE_DIR)

	lcov --capture --directory . --exclude '/usr/*' --output-file $(COVERAGE_DIR)/coverage.info

	genhtml $(COVERAGE_DIR)/coverage.info --output-directory $(COVERAGE_DIR)

libmcPolymer: $(MCPSIM_SO)

libcempoly: $(CEMPOLY_SO)

# c source

$(BUILD_DIR)/%.c.o: %.c

	$(MKDIR_P) $(dir $@)

	$(CC) $(CPPFLAGS) $(CFLAGS) $(COVERAGE) -c $< -o $@

# c++ source

$(BUILD_DIR)/%.cpp.o: %.cpp

	$(MKDIR_P) $(dir $@)

	$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(COVERAGE) -c $< -o $@

.PHONY: clean

clean:

	$(RM) -r $(BUILD_DIR)

	$(RM) -r $(LOG_DIR)

	$(RM) -r $(COVERAGE_DIR)/*

	$(RM) $(TARGET_EXEC)

	$(RM) $(KMCTEST_EXEC)

	$(RM) $(GTEST_EXEC)

	$(RM) $(CEMPOLY_EXEC)

	$(RM) $(DBUSSERVER_EXEC)

	$(RM) $(ANALYSIS_EXEC)

-include $(DEPS)

MKDIR_P ?= mkdir -p

// MersenneTwister.h

// Mersenne Twister random number generator -- a C++ class MTRand

// Based on code by Makoto Matsumoto, Takuji Nishimura, and Shawn Cokus

// Richard J. Wagner  v1.1  28 September 2009  wagnerr@umich.edu

// The Mersenne Twister is an algorithm for generating random numbers.  It

// was designed with consideration of the flaws in various other generators.

// The period, 2^19937-1, and the order of equidistribution, 623 dimensions,

// are far greater.  The generator is also fast; it avoids multiplication and

// division, and it benefits from caches and pipelines.  For more information

// see the inventors' web page at

// http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/emt.html

// Reference

// M. Matsumoto and T. Nishimura, "Mersenne Twister: A 623-Dimensionally

// Equidistributed Uniform Pseudo-Random Number Generator", ACM Transactions on

// Modeling and Computer Simulation, Vol. 8, No. 1, January 1998, pp 3-30.

// Copyright (C) 1997 - 2002, Makoto Matsumoto and Takuji Nishimura,

// Copyright (C) 2000 - 2009, Richard J. Wagner

// All rights reserved.

// 

// Redistribution and use in source and binary forms, with or without

// modification, are permitted provided that the following conditions

// are met:

// 

//   1. Redistributions of source code must retain the above copyright

//      notice, this list of conditions and the following disclaimer.

//

//   2. Redistributions in binary form must reproduce the above copyright

//      notice, this list of conditions and the following disclaimer in the

//      documentation and/or other materials provided with the distribution.

//

//   3. The names of its contributors may not be used to endorse or promote 

//      products derived from this software without specific prior written 

//      permission.

// 

// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"

// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE

// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE

// ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE

// LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR

// CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF

// SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS

// INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN

// CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)

// ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE

// POSSIBILITY OF SUCH DAMAGE.

// The original code included the following notice:

// 

//     When you use this, send an email to: m-mat@math.sci.hiroshima-u.ac.jp

//     with an appropriate reference to your work.

// 

// It would be nice to CC: wagnerr@umich.edu and Cokus@math.washington.edu

// when you write.

#pragma once

// Not thread safe (unless auto-initialization is avoided and each thread has

// its own MTRand object)

#include <iostream>

#include <climits>

#include <cstdio>

#include <ctime>

#include <cmath>

class MTRand {

// Data

public:

	typedef unsigned long uint32;  // integer type, at least 32 bits

	enum { N = 624 };       // length of state vector

	enum { SAVE = N + 1 };  // length of array for save()

protected:

	enum { M = 397 };  // period parameter

	uint32 state[N];   // internal state

	uint32 *pNext;     // next value to get from state

	int left;          // number of values left before reload needed

// Methods

public:

	MTRand( const uint32 oneSeed );  // initialize with a simple uint32

	MTRand( uint32 *const bigSeed, uint32 const seedLength = N );  // or array

	MTRand();  // auto-initialize with /dev/urandom or time() and clock()

	MTRand( const MTRand& o );  // copy

	// Do NOT use for CRYPTOGRAPHY without securely hashing several returned

	// values together, otherwise the generator state can be learned after

	// reading 624 consecutive values.

	// Access to 32-bit random numbers

	uint32 randInt();                     // integer in [0,2^32-1]

	uint32 randInt( const uint32 n );     // integer in [0,n] for n < 2^32

	double rand();                        // real number in [0,1]

	double rand( const double n );        // real number in [0,n]

	double randExc();                     // real number in [0,1)

	double randExc( const double n );     // real number in [0,n)

	double randDblExc();                  // real number in (0,1)

	double randDblExc( const double n );  // real number in (0,n)

	double operator()();                  // same as rand()

	// Access to 53-bit random numbers (capacity of IEEE double precision)

	double rand53();  // real number in [0,1)

	// Access to nonuniform random number distributions

	double randNorm( const double mean = 0.0, const double stddev = 1.0 );

	// Re-seeding functions with same behavior as initializers

	void seed( const uint32 oneSeed );

	void seed( uint32 *const bigSeed, const uint32 seedLength = N );

	void seed();

	// Saving and loading generator state

	void save( uint32* saveArray ) const;  // to array of size SAVE

	void load( uint32 *const loadArray );  // from such array

	friend std::ostream& operator<<( std::ostream& os, const MTRand& mtrand );

	friend std::istream& operator>>( std::istream& is, MTRand& mtrand );

	MTRand& operator=( const MTRand& o );

protected:

	void initialize( const uint32 oneSeed );

	void reload();

	uint32 hiBit( const uint32 u ) const { return u & 0x80000000UL; }

	uint32 loBit( const uint32 u ) const { return u & 0x00000001UL; }

	uint32 loBits( const uint32 u ) const { return u & 0x7fffffffUL; }

	uint32 mixBits( const uint32 u, const uint32 v ) const

		{ return hiBit(u) | loBits(v); }

	uint32 magic( const uint32 u ) const

		{ return loBit(u) ? 0x9908b0dfUL : 0x0UL; }

	uint32 twist( const uint32 m, const uint32 s0, const uint32 s1 ) const

		{ return m ^ (mixBits(s0,s1)>>1) ^ magic(s1); }

	static uint32 hash( time_t t, clock_t c );

};

// Functions are defined in order of usage to assist inlining

inline MTRand::uint32 MTRand::hash( time_t t, clock_t c )

{

	// Get a uint32 from t and c

	// Better than uint32(x) in case x is floating point in [0,1]

	// Based on code by Lawrence Kirby (fred@genesis.demon.co.uk)

	static uint32 differ = 0;  // guarantee time-based seeds will change

	uint32 h1 = 0;

	unsigned char *p = (unsigned char *) &t;

	for( size_t i = 0; i < sizeof(t); ++i )

	{

		h1 *= UCHAR_MAX + 2U;

		h1 += p[i];

	}

	uint32 h2 = 0;

	p = (unsigned char *) &c;

	for( size_t j = 0; j < sizeof(c); ++j )

	{

		h2 *= UCHAR_MAX + 2U;

		h2 += p[j];

	}

	return ( h1 + differ++ ) ^ h2;

}

inline void MTRand::initialize( const uint32 seed )

{

	// Initialize generator state with seed

	// See Knuth TAOCP Vol 2, 3rd Ed, p.106 for multiplier.

	// In previous versions, most significant bits (MSBs) of the seed affect

	// only MSBs of the state array.  Modified 9 Jan 2002 by Makoto Matsumoto.

	uint32 *s = state;

	uint32 *r = state;

	int i = 1;

	*s++ = seed & 0xffffffffUL;

	for( ; i < N; ++i )

	{

		*s++ = ( 1812433253UL * ( *r ^ (*r >> 30) ) + i ) & 0xffffffffUL;

		r++;

	}

}

inline void MTRand::reload()

{

	// Generate N new values in state

	// Made clearer and faster by Matthew Bellew (matthew.bellew@home.com)

	static const int MmN = int(M) - int(N);  // in case enums are unsigned

	uint32 *p = state;

	int i;

	for( i = N - M; i--; ++p )

		*p = twist( p[M], p[0], p[1] );

	for( i = M; --i; ++p )

		*p = twist( p[MmN], p[0], p[1] );

	*p = twist( p[MmN], p[0], state[0] );

	left = N, pNext = state;

}

inline void MTRand::seed( const uint32 oneSeed )

{

	// Seed the generator with a simple uint32

	initialize(oneSeed);

	reload();

}

inline void MTRand::seed( uint32 *const bigSeed, const uint32 seedLength )

{

	// Seed the generator with an array of uint32's

	// There are 2^19937-1 possible initial states.  This function allows

	// all of those to be accessed by providing at least 19937 bits (with a

	// default seed length of N = 624 uint32's).  Any bits above the lower 32

	// in each element are discarded.

	// Just call seed() if you want to get array from /dev/urandom

	initialize(19650218UL);

	int i = 1;

	uint32 j = 0;

	int k = ( N > seedLength ? N : seedLength );

	for( ; k; --k )

	{

		state[i] =

		state[i] ^ ( (state[i-1] ^ (state[i-1] >> 30)) * 1664525UL );

		state[i] += ( bigSeed[j] & 0xffffffffUL ) + j;

		state[i] &= 0xffffffffUL;

		++i;  ++j;

		if( i >= N ) { state[0] = state[N-1];  i = 1; }

		if( j >= seedLength ) j = 0;

	}

	for( k = N - 1; k; --k )

	{

		state[i] =

		state[i] ^ ( (state[i-1] ^ (state[i-1] >> 30)) * 1566083941UL );

		state[i] -= i;

		state[i] &= 0xffffffffUL;

		++i;

		if( i >= N ) { state[0] = state[N-1];  i = 1; }

	}

	state[0] = 0x80000000UL;  // MSB is 1, assuring non-zero initial array

	reload();

}

inline void MTRand::seed()

{

	// Seed the generator with an array from /dev/urandom if available

	// Otherwise use a hash of time() and clock() values

	// First try getting an array from /dev/urandom

	//FILE* urandom = fopen( "/dev/urandom", "rb" );

	/*

	if( urandom )

	{

		uint32 bigSeed[N];

		register uint32 *s = bigSeed;

		register int i = N;

		register bool success = true;

		while( success && i-- )

			success = fread( s++, sizeof(uint32), 1, urandom );

		fclose(urandom);

		if( success ) { seed( bigSeed, N );  return; }

	}

	*/

	// Was not successful, so use time() and clock() instead

	seed( hash( time(NULL), clock() ) );

}

inline MTRand::MTRand( const uint32 oneSeed )

	{ seed(oneSeed); }

inline MTRand::MTRand( uint32 *const bigSeed, const uint32 seedLength )

	{ seed(bigSeed,seedLength); }

inline MTRand::MTRand()

	{ seed(); }

inline MTRand::MTRand( const MTRand& o )

{

	const uint32 *t = o.state;

	uint32 *s = state;

	int i = N;

	for( ; i--; *s++ = *t++ ) {}

	left = o.left;

	pNext = &state[N-left];

}

inline MTRand::uint32 MTRand::randInt()

{

	// Pull a 32-bit integer from the generator state

	// Every other access function simply transforms the numbers extracted here

	if( left == 0 ) reload();

	--left;

	uint32 s1;

	s1 = *pNext++;

	s1 ^= (s1 >> 11);

	s1 ^= (s1 <<  7) & 0x9d2c5680UL;

	s1 ^= (s1 << 15) & 0xefc60000UL;

	return ( s1 ^ (s1 >> 18) );

}

inline MTRand::uint32 MTRand::randInt( const uint32 n )

{

	// Find which bits are used in n

	// Optimized by Magnus Jonsson (magnus@smartelectronix.com)

	uint32 used = n;

	used |= used >> 1;

	used |= used >> 2;

	used |= used >> 4;

	used |= used >> 8;

	used |= used >> 16;

	// Draw numbers until one is found in [0,n]

	uint32 i;

	do

		i = randInt() & used;  // toss unused bits to shorten search

	while( i > n );

	return i;

}

inline double MTRand::rand()

	{ return double(randInt()) * (1.0/4294967295.0); }

inline double MTRand::rand( const double n )

	{ return rand() * n; }

inline double MTRand::randExc()

	{ return double(randInt()) * (1.0/4294967296.0); }

inline double MTRand::randExc( const double n )

	{ return randExc() * n; }

inline double MTRand::randDblExc()

	{ return ( double(randInt()) + 0.5 ) * (1.0/4294967296.0); }

inline double MTRand::randDblExc( const double n )

	{ return randDblExc() * n; }

inline double MTRand::rand53()

{

	uint32 a = randInt() >> 5, b = randInt() >> 6;

	return ( a * 67108864.0 + b ) * (1.0/9007199254740992.0);  // by Isaku Wada

}

inline double MTRand::randNorm( const double mean, const double stddev )

{

	// Return a real number from a normal (Gaussian) distribution with given

	// mean and standard deviation by polar form of Box-Muller transformation

	double x, y, r;

	do

	{

		x = 2.0 * rand() - 1.0;

		y = 2.0 * rand() - 1.0;

		r = x * x + y * y;

	}

	while ( r >= 1.0 || r == 0.0 );

	double s = sqrt( -2.0 * log(r) / r );

	return mean + x * s * stddev;

}

inline double MTRand::operator()()

{

	return rand();

}

inline void MTRand::save( uint32* saveArray ) const

{

	const uint32 *s = state;

	uint32 *sa = saveArray;

	int i = N;

	for( ; i--; *sa++ = *s++ ) {}

	*sa = left;

}

inline void MTRand::load( uint32 *const loadArray )

{

	uint32 *s = state;

	uint32 *la = loadArray;

	int i = N;

	for( ; i--; *s++ = *la++ ) {}

	left = *la;

	pNext = &state[N-left];

}

inline std::ostream& operator<<( std::ostream& os, const MTRand& mtrand )

{

	const MTRand::uint32 *s = mtrand.state;

	int i = mtrand.N;

	for( ; i--; os << *s++ << "\t" ) {}

	return os << mtrand.left;

}

inline std::istream& operator>>( std::istream& is, MTRand& mtrand )

{

	MTRand::uint32 *s = mtrand.state;

	int i = mtrand.N;

	for( ; i--; is >> *s++ ) {}

	is >> mtrand.left;

	mtrand.pNext = &mtrand.state[mtrand.N-mtrand.left];

	return is;

}

inline MTRand& MTRand::operator=( const MTRand& o )

{

	if( this == &o ) return (*this);

	const uint32 *t = o.state;

	uint32 *s = state;

	int i = N;

	for( ; i--; *s++ = *t++ ) {}

	left = o.left;

	pNext = &state[N-left];

	return (*this);

}

// Change log:

//

// v0.1 - First release on 15 May 2000

//      - Based on code by Makoto Matsumoto, Takuji Nishimura, and Shawn Cokus

//      - Translated from C to C++

//      - Made completely ANSI compliant

//      - Designed convenient interface for initialization, seeding, and

//        obtaining numbers in default or user-defined ranges

//      - Added automatic seeding from /dev/urandom or time() and clock()

//      - Provided functions for saving and loading generator state

//

// v0.2 - Fixed bug which reloaded generator one step too late

//

// v0.3 - Switched to clearer, faster reload() code from Matthew Bellew

//

// v0.4 - Removed trailing newline in saved generator format to be consistent

//        with output format of built-in types

//

// v0.5 - Improved portability by replacing static const int's with enum's and

//        clarifying return values in seed(); suggested by Eric Heimburg

//      - Removed MAXINT constant; use 0xffffffffUL instead

//

// v0.6 - Eliminated seed overflow when uint32 is larger than 32 bits

//      - Changed integer [0,n] generator to give better uniformity

//

// v0.7 - Fixed operator precedence ambiguity in reload()

//      - Added access for real numbers in (0,1) and (0,n)

//

// v0.8 - Included time.h header to properly support time_t and clock_t

//

// v1.0 - Revised seeding to match 26 Jan 2002 update of Nishimura and Matsumoto

//      - Allowed for seeding with arrays of any length

//      - Added access for real numbers in [0,1) with 53-bit resolution

//      - Added access for real numbers from normal (Gaussian) distributions

//      - Increased overall speed by optimizing twist()

//      - Doubled speed of integer [0,n] generation

//      - Fixed out-of-range number generation on 64-bit machines

//      - Improved portability by substituting literal constants for long enum's

//      - Changed license from GNU LGPL to BSD

//

// v1.1 - Corrected parameter label in randNorm from "variance" to "stddev"

//      - Changed randNorm algorithm from basic to polar form for efficiency